2GTF | pdb_00002gtf

Crystal structure of nitrophorin 2 complex with pyrimidine

• PDB DOI: https://doi.org/10.2210/pdb2GTF/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Rhodnius prolixus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-04-27 Released: 2007-03-13 
• Deposition Author(s): Weichsel, A., Montfort, W.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.211 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

Crystal structures, ligand induced conformational change and heme deformation in complexes of nitrophorin 2, a nitric oxide transport protein from rhodnius prolixus

Weichsel, A., Berry, R.E., Walker, F.A., Montfort, W.R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 20.78 kDa 
• Atom Count: 1,651 
• Modeled Residue Count: 180 
• Deposited Residue Count: 180 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nitrophorin-2	A [auth X]	180	Rhodnius prolixus	Mutation(s): 0
UniProt
Find proteins for Q26241 (Rhodnius prolixus) Explore Q26241  Go to UniProtKB:  Q26241

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HEM	B [auth X]	PROTOPORPHYRIN IX CONTAINING FE C34 H32 Fe N4 O4 KABFMIBPWCXCRK-RGGAHWMASA-L
P1R	C [auth X]	PYRIMIDINE C4 H4 N2 CZPWVGJYEJSRLH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.211 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.374	α = 90
b = 34.374	β = 90
c = 255.82	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDISPLAYF	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-13 
Deposition Author(s): Weichsel, A., Montfort, W.R.

Revision History  

• Version 1.0: 2007-03-13
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-10-16
  Changes: Structure summary